Is this just the nature of the beast or do I have a primary chain adjustment issue. This is on a 2012 dyna. And my clutch is perfect. Any input is appreciated

 

Good chance your clutch needs adjust. Check free play at the handle first. If that don't work with bike cold adjust clutch pack. Also, if primary oil is not allowing a smooth separation of the plates this could cause drag.

 

Adjusted clutch last week everything is cool with the clutch . Sometimes I hear noise coming from the primary

 

By design the stock mainshaft weighs almost 6 pounds because they incorporated the first 4 gears as an integral part of the main shaft. In short it is all one big heavy piece and is going to have a louder clunk then it's five speed predecessor that was less then half the weight. Clutch adjustment and primary chain tension can also be factors. If these are set to spec and you still have a clunk then you can live with it, try different oil or try our 7 speed. We also having a bearing door and a smooth shift kit as other options to help.